Hi Asfa,
I believe you are already using the best force fields available,so its
likely that the problem has a different root. Can you give more
details of your simulation?
Gustavo.
On Wednesday, June 9, 2010, Asfa Ali <asfa.iisc.gmail.com> wrote:
> Hi,
>
> I am using AmberTools 1.3 along with Amber 9 package. I did MD for rna using
> forcefields leaprc.ff99bsc0 as well as leaprc.ff99SB, however in both the
> cases the rna structure opens into two strands at the beginning of the
> production run (without any restraint).
>
> What forcefield should I use in order to keep the structure intact?
>
> Kindly help.
>
> Asfa.
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--
Gustavo Seabra
Professor Adjunto
Departamento de Química Fundamental
Universidade Federal de Pernambuco
Fone: +55-81-2126-7417
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Received on Wed Jun 09 2010 - 04:30:11 PDT
